The crisprVerse is a collection of packages for CRISPR guide RNA (gRNA) design that can easily be installed
with the crisprVerse package. This provides
a convenient way of downloading and installing all crisprVerse packages
with a single R command.
The package can be installed from the Bioconductor devel branch using the following commands in an R session:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version="devel")
BiocManager::install("crisprVerse")The core crisprVerse includes the packages that are commonly used for
gRNA design, and are attached when you attach the crisprVerse package:
library(crisprVerse)You can check that all crisprVerse packages are up-to-date
with the function crisprVerse_update().
The following packages are installed and loaded with the crisprVerse package:
GuideSet objects.sessionInfo()## R Under development (unstable) (2024-10-26 r87273 ucrt)
## Platform: x86_64-w64-mingw32/x64
## Running under: Windows Server 2022 x64 (build 20348)
##
## Matrix products: default
##
##
## locale:
## [1] LC_COLLATE=C
## [2] LC_CTYPE=English_United States.utf8
## [3] LC_MONETARY=English_United States.utf8
## [4] LC_NUMERIC=C
## [5] LC_TIME=English_United States.utf8
##
## time zone: America/New_York
## tzcode source: internal
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] crisprViz_1.9.0 crisprDesign_1.9.0 crisprScore_1.11.0
## [4] crisprScoreData_1.9.0 ExperimentHub_2.15.0 AnnotationHub_3.15.0
## [7] BiocFileCache_2.15.0 dbplyr_2.5.0 BiocGenerics_0.53.1
## [10] generics_0.1.3 crisprBowtie_1.11.0 crisprBase_1.11.0
## [13] crisprVerse_1.9.0 BiocStyle_2.35.0
##
## loaded via a namespace (and not attached):
## [1] RColorBrewer_1.1-3 rstudioapi_0.17.1
## [3] jsonlite_1.8.9 magrittr_2.0.3
## [5] GenomicFeatures_1.59.0 rmarkdown_2.28
## [7] BiocIO_1.17.0 zlibbioc_1.53.0
## [9] vctrs_0.6.5 memoise_2.0.1
## [11] Rsamtools_2.23.0 RCurl_1.98-1.16
## [13] base64enc_0.1-3 htmltools_0.5.8.1
## [15] S4Arrays_1.7.1 progress_1.2.3
## [17] curl_5.2.3 SparseArray_1.7.0
## [19] Formula_1.2-5 sass_0.4.9
## [21] bslib_0.8.0 htmlwidgets_1.6.4
## [23] basilisk_1.19.0 Gviz_1.51.0
## [25] httr2_1.0.5 cachem_1.1.0
## [27] GenomicAlignments_1.43.0 lifecycle_1.0.4
## [29] pkgconfig_2.0.3 Matrix_1.7-1
## [31] R6_2.5.1 fastmap_1.2.0
## [33] GenomeInfoDbData_1.2.13 MatrixGenerics_1.19.0
## [35] digest_0.6.37 colorspace_2.1-1
## [37] AnnotationDbi_1.69.0 S4Vectors_0.45.0
## [39] Hmisc_5.2-0 GenomicRanges_1.59.0
## [41] RSQLite_2.3.7 filelock_1.0.3
## [43] randomForest_4.7-1.2 fansi_1.0.6
## [45] httr_1.4.7 abind_1.4-8
## [47] compiler_4.5.0 Rbowtie_1.47.0
## [49] bit64_4.5.2 backports_1.5.0
## [51] htmlTable_2.4.3 BiocParallel_1.41.0
## [53] DBI_1.2.3 biomaRt_2.63.0
## [55] rappdirs_0.3.3 DelayedArray_0.33.1
## [57] rjson_0.2.23 tools_4.5.0
## [59] foreign_0.8-87 nnet_7.3-19
## [61] glue_1.8.0 restfulr_0.0.15
## [63] grid_4.5.0 checkmate_2.3.2
## [65] cluster_2.1.6 gtable_0.3.6
## [67] BSgenome_1.75.0 tzdb_0.4.0
## [69] ensembldb_2.31.0 data.table_1.16.2
## [71] hms_1.1.3 xml2_1.3.6
## [73] utf8_1.2.4 XVector_0.47.0
## [75] BiocVersion_3.21.1 pillar_1.9.0
## [77] stringr_1.5.1 dplyr_1.1.4
## [79] lattice_0.22-6 deldir_2.0-4
## [81] rtracklayer_1.67.0 bit_4.5.0
## [83] biovizBase_1.55.0 tidyselect_1.2.1
## [85] Biostrings_2.75.0 knitr_1.48
## [87] gridExtra_2.3 bookdown_0.41
## [89] ProtGenerics_1.39.0 IRanges_2.41.0
## [91] SummarizedExperiment_1.37.0 stats4_4.5.0
## [93] xfun_0.49 Biobase_2.67.0
## [95] matrixStats_1.4.1 stringi_1.8.4
## [97] UCSC.utils_1.3.0 lazyeval_0.2.2
## [99] yaml_2.3.10 evaluate_1.0.1
## [101] codetools_0.2-20 interp_1.1-6
## [103] tibble_3.2.1 BiocManager_1.30.25
## [105] cli_3.6.3 rpart_4.1.23
## [107] reticulate_1.39.0 munsell_0.5.1
## [109] jquerylib_0.1.4 dichromat_2.0-0.1
## [111] Rcpp_1.0.13-1 GenomeInfoDb_1.43.0
## [113] dir.expiry_1.15.0 png_0.1-8
## [115] XML_3.99-0.17 parallel_4.5.0
## [117] ggplot2_3.5.1 readr_2.1.5
## [119] blob_1.2.4 basilisk.utils_1.19.0
## [121] prettyunits_1.2.0 jpeg_0.1-10
## [123] latticeExtra_0.6-30 AnnotationFilter_1.31.0
## [125] bitops_1.0-9 txdbmaker_1.3.0
## [127] VariantAnnotation_1.53.0 scales_1.3.0
## [129] crayon_1.5.3 rlang_1.1.4
## [131] KEGGREST_1.47.0